SUMMARY Gametes are among the most highly specialized cells produced during development. Although gametogenesis culminates in transcriptional quiescence in plants and animals, regulatory mechanisms controlling this are unknown. Here, we confirm that gamete differentiation in the single-celled yeast Saccharomyces cerevisiae is accompanied by global transcriptional shutoff following the completion of meiosis. We show that Jhd2, a highly conserved JARID1-family histone H3K4 demethylase, activates protein-coding gene transcription in opposition to this programmed transcriptional shutoff, sustaining the period of productive transcription during spore differentiation. Moreover, using genome-wide nucleosome, H3K4me, and transcript mapping experiments, we demonstrate that JHD2 globally represses intergenic noncoding transcription during this period. The widespread transcriptional defects of JHD2 mutants are associated with precocious differentiation and the production of stress-sensitive spores, demonstrating that Jhd2 regulation of the global postmeiotic transcriptional program is critical for the production of healthy meiotic progeny.

Much of euchromatin regulation occurs through reversible methylation of histone H3 lysine-4 and lysine-36 (H3K4me and H3K36me). Using the budding yeast Saccharomyces cerevisiae, we previously found that levels of H3K4me modulated temperature sensitive alleles of the transcriptional elongation complex Spt6-Spn1 through an unknown H3K4me effector pathway. Here we identify the Rpd3S histone deacetylase complex as the H3K4me effector underlying these Spt6-Spn1 genetic interactions. Exploiting these Spt6-Spn1 genetic interactions, we show that H3K4me and H3K36me collaboratively impact Rpd3S function in an opposing manner. H3K36me is deposited by the histone methyltransferase Set2 and is known to promote Rpd3S function at RNA PolII transcribed open reading frames. Using genetic epistasis experiments, we find that mutations perturbing the Set2-H3K36me-Rpd3S pathway suppress the growth defects caused by temperature sensitive alleles of SPT6 and SPN1, illuminating that this pathway antagonizes Spt6-Spn1. Using these sensitive genetic assays, we also identify a role for H3K4me in antagonizing Rpd3S that functions through the Rpd3S subunit Rco1, which is known to bind H3 N-terminal tails in a manner that is prevented by H3K4me. Further genetic experiments reveal that the H3K4 and H3K36 demethylases JHD2 and RPH1 mediate this combinatorial control of Rpd3S. Finally, our studies also show that the Rpd3L complex, which acts at promoter-proximal regions of PolII transcribed genes, counters Rpd3S for genetic modulation of Spt6-Spn1, and that these two Rpd3 complexes balance the activities of each other. Our findings present the first evidence that H3K4me and H3K36me act combinatorially to control Rpd3S.

1Much of euchromatin regulation occurs through reversible methylation of histone H3 2 lysine-4 and lysine-36 (H3K4me and H3K36me). Using the budding yeast Saccharomyces 3 cerevisiae, we previously found that levels of H3K4me modulated temperature sensitive alleles 4 of the transcriptional elongation complex Spt6-Spn1 through an unknown H3K4me effector 5 pathway. Here we identify the Rpd3S histone deacetylase complex as the H3K4me effector 6 underlying these Spt6-Spn1 genetic interactions. Exploiting these Spt6-Spn1 genetic interactions, 7we show that H3K4me and H3K36me collaboratively impact Rpd3S function in an opposing 8 manner. H3K36me is deposited by the histone methyltransferase Set2 and is known to promote 9Rpd3S function at RNA PolII transcribed open reading frames. Using genetic epistasis 10 experiments, we find that mutations perturbing the Set2-H3K36me-Rpd3S pathway suppress the 11 growth defects caused by temperature sensitive alleles of SPT6 and SPN1, illuminating that this 12 pathway antagonizes Spt6-Spn1. Using these sensitive genetic assays, we also identify a role for 13H3K4me in antagonizing Rpd3S that functions through the Rpd3S subunit Rco1, which is known 14 to bind H3 N-terminal tails in a manner that is prevented by H3K4me. Further genetic 15 experiments reveal that the H3K4 and H3K36 demethylases JHD2 and RPH1 mediate this 16 combinatorial control of Rpd3S. Finally, our studies also show that the Rpd3L complex, which 17 acts at promoter-proximal regions of PolII transcribed genes, counters Rpd3S for genetic 18 modulation of Spt6-Spn1, and that these two Rpd3 complexes balance the activities of each 19 other. Our findings present the first evidence that H3K4me and H3K36me act combinatorially to 20 control Rpd3S. 21 22